Template developed with materials from https://hbctraining.github.io/main/.

This code is in this revision.

1 Overview

  • Project: name_hbcXXXXX
  • PI: person name
  • Analyst: person in the core
  • Experiment: short description
  • Aim: short description

2 MAST analysis

Pre-processing

Subset genes observed in at least 10% of cells …

Prep for MAST comparison …

MAST run with desired contrasts …

Output results …

[Full MAST object saved]

[MAST summary results output to csv files]

[Significant MAST summary results output to csv files]

2.1 Differentially Expressed Genes Table

[Option 1: numbers displayed in digits]

[Option 2: FDR displayed in scientific notation]

2.2 Group Mean Heatmap

2.2.1 age

2.3 Volcano plot and Top DEG

This volcano plot shows the genes that are significantly up- and down-regulated as a result of the analysis comparison.

The points highlighted:

  • in grey points are non-significant.
  • in blue have a padj > 0.05 and a log2-fold change > 0.5.
  • in plum have a padj < 0.05 and a log2-fold change < 0.5.
  • in purple are genes that have fdr < 0.05 and a log2-fold change > 0.5.

The dashed lines correspond to the cutoff values of log2 foldchance and padj that we have chosen.

2.3.1 age

2.4 % of expression for Top DEGs

2.5 Plain sc-expression across contrast groups: top 16 DEGs

2.5.1 HLA-B

2.5.2 SAT1

2.5.3 PERP

2.5.4 CD74

2.5.5 IGFBP5

2.5.6 KRT10

2.5.7 MT-CYB

2.5.8 MT-ND1

2.5.9 H2AFZ

2.5.10 ADIRF

2.5.11 CAV1

2.5.12 CCL19

2.5.13 CCL21

2.5.14 MT-ATP6

2.5.15 PFN1

2.5.16 TPPP3

2.6 Colored sc-expression across contrast groups: top 16 DEGs

2.6.1 HLA-B

2.6.2 SAT1

2.6.3 PERP

2.6.4 CD74

2.6.5 IGFBP5

2.6.6 KRT10

2.6.7 MT-CYB

2.6.8 MT-ND1

2.6.9 H2AFZ

2.6.10 ADIRF

2.6.11 CAV1

2.6.12 CCL19

2.6.13 CCL21

2.6.14 MT-ATP6

2.6.15 PFN1

2.6.16 TPPP3

2.7 Dot styles: sc-expression across contrast groups

2.7.1 quasirandom

2.7.2 dotplot

2.7.3 jitter

3 R session

List and version of tools used for the QC report generation.